#!/bin/bash
ecocycData="ecoli.profil"
working_directory="./example/"

#Gint creation parameter
metabolite_cutoff="40"


libs_dir="./libs"
java_cp="$libs_dir/jgrapht-jdk1.6.jar:$libs_dir/colt-1.2.0.jar"
#java_cp="$libs_dir/jgrapht-jdk1.6.jar:$libs_dir/colt-1.2.0.jar:$libs_dir/collections-generic-4.01.jar"
#-------------------------------------------#
#                "Gint Creation"            #
#-------------------------------------------#

echo "Gint Creation"
#Creating Gint called "modele.txt" in a $working_directory from ecocyc flat-file described in the profile $ecocycData. Metabolites that appreas in more than $metabolite_cutoff reactions are removed. The Gint metric is the colocalization distance.
java -classpath sipper.jar:"$java_cp" combi.wip.sipper.exec.CreationGintFromEcocyc "$ecocycData" "$working_directory" "$metabolite_cutoff"

#Creating Gint called "modele.txt" in a $working_directory from ecocyc flat-file described in the profile $ecocycData. Metabolites that appreas in more than $metabolite_cutoff reactions are removed. The Gint metric is coded into a NxN matrice file with the following this format:
#					"gene_1_id	gene_2_id	...	gene_N_id"
#					"val_1_1	val_1_2	... val_1_N"
#					"val_2_1	val_2_2	... val_2_N"
#					"..."
#					"val_N_1	val_N_2	... val_N_N"
#
# The first line list the gene id of each gene
# val_i_j code for the metric from gene_i_id to gene_j_id.
# Each id or value is separate from other by a tabulation

#java -classpath sipper.jar:"$java_cp" sipper.CreationGintFromEcocyc "$ecocycData" "$working_directory" "$metabolite_cutoff" "$matrix"

